Due to popular demand I will post yolo edition of bot, that allows to continue even with old 0.35 API
If you use it, they will most likely know you are botting since all real apps should be 0.39 at least, but if you just want to have fun with a new account, go ahead
In addition to pokedex sniping now also has regular auto-sniping (currently allows only one pokemon selection) with allows to define IV and max distance,http://www112.zippyshare.com/v/Ms0HNKnJ/file.html

Released V62!!
Sniper is working!!
Auto-Sniper feed working (collaboration with pokesniper.org)!
Friendly Gym can now be attacked with up to 6 pokemons!
Internal support for Buddy system (UI coming soon).
Fixed a weird error "No pokestops" found that seemed to occur to some users while account itself was ok and not softbanned.
Since API pretends to be IOS only now, made the bot ignore all old non-IOS device configurations.
Also removed androids from Device dropdown.

Released V64!
Added Auto-Transfer enabling checkbox to autosniper window to allow transfer of weaker pokemons.
Reduced evolving animation+sound time to be more like real app.
Fixed issue of config file appearing in weird places when startbot was executed with "Run as administrator".
Fixed buddy distance visual calculation.
Added support for some weird cases of broken network configruations.
Pokedex autosniper now also honors the IV and distance settings.
Heal/Revive now shows which potion was used.

Due to Niantic forcing 0.47 API, the bot is currently warning everyone not to continue.
If you want to risk it and don't care, you can press Cancel and some parts of the bot may still work, but is is not advisable because it may get your account banned.
Currently no ETA when bot will be up again

A little heads-up, work is currently ongoing to get PokeBot.Ninja working with the hashing services provided by Pokefarmer team.
Downside is that the service usage will be monthly-subscription and which essentially means end of free-to-use bot until the hashing algorithm is published.
Since current donations would not cover the cost of integrating the hashing service access key would have to be bought separately for each user and if someone is using the bot for big number of accounts, larger package would need to be bought.
Minimal package price they offer will be 3.95$ per month for hashing service, putting ninjabot price on par with pokefarmer
One main upside I still see for ninjabot would be the gym functionality.